[phenixbb] Help with using FFT map coefficients tool

Emilia C. Arturo (Emily) eca38 at drexel.edu
Mon Jun 1 08:49:38 PDT 2015


The command line steps you gave worked well (i.e. I got the map I wanted)
for the models in which I am interested.

But the GUI is still giving the same error  "This reflections file does not
appear to contain any suitable map coefficients", even for the PDB id you
gave as an example (1AKG). This is what I did to use the GUI: I typed in
the PDB id to the GUI 'Reflections tools' > 'Import CIF structure factors'
tool, and the tool fetched the model and .cif file and output an mtz file.
But when I loaded this mtz file into the GUI 'Maps' > 'FFT map
coefficients' tool, I got the error. Furthermore, EVEN if I loaded the mtz
file that I'd generated using the command line phenix.maps 1akg.{pdb,mtz}
into the GUI maps tool, I get the same error.

I am fine using the command line, but I suspect that there's an issue with
how the GUI is loading the mtz files for the Maps tool.


step 1 - get files from PDB:
> phenix.fetch_pdb 1akg --mtz
> step 2 - compute maps:
> phenix.maps 1akg.{pdb,mtz}
> step 3 - convert map coefficients into map:
> phenix.mtz2map 1akg_map_coeffs.mtz

> Let me know if you still having problems with this and I will send
> step-by-step instructions how to do this using the GUI.
> Pavel
> On 5/30/15 3:05 PM, Emilia C. Arturo (Emily) wrote:
>  Hello.
>  I'd like to generate a map appropriate for viewing in PyMOL, using a
> model and structure factors downloaded from the PDB. But I'm unable to do
> so, and perhaps you can help me figure out what I might be doing wrong:
>  To generate the map, I did the following using the phenix GUI (version
> 1.9-1692):
> 1. I used Reflection tools > Import CIF structure factors to convert the
> .cif format structure factors for PDB id 1J8U to an mtz file.
> 2. Then, to configure the job to generate the CCP4 map, I loaded this mtz
> file, but when I did that I got the following error:
> "This reflections file does not appear to contain any suitable map
> coefficients"
>  I went through the same steps again for two other PDB ids, this time
> generating the mtz file by either letting phenix do it from a PDB id, or by
> supplying the tool with both a .cif file with structure factors and a pdb
> model file. I get the same error.
> Has anyone any advice?
>  Regards,
> Emily.
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